You get per-turn trade income from each trade route regardless of where it is. It makes more money the closer it is to the destination planet and less money the closer it is to the planet of origin - they average out to the value you see when you first make the trade route. Because of this averaging effect, it doesn't matter what the speed of the freighter is, because the average income would always be the same (well, it might affect gameplay if the freighter has a really fast speed and is able to, at least temporarily, outrun enemy ships as it travels along the trade route, but the enemy would just have to remain in place and destroy the freighter as it came back). Just think of the freighter as an avatar of the trade route and not an independent freighter in itself and everything becomes much clearer
Also - whatever stats your trade ship had when you first sent it to its destination planet, even if it was a battleship with a trade module stuck onto it as an afterthought, it loses all of its speed, attack, defense, and hull strength when it becomes a mini-freighter.
As for protecting your trade routes, the only realistic options are to:
1.) Get Galactic Privateers (the best option, and you can get it before the AI if you try hard).
2.) Keep the trade routes away from your enemies - if you must run it through enemy territory, then be prepared to lose it or suffer losses defending it. If possible, keep them away from the border planets of another country, as those are usually the first captured or converted in a military or cultural war.
3.) Build a rapid-response team to police some of the trade routes - put as many engines, sensors, and weapons as you can on a few frigates or cruisers, and patrol the trade routes, or at least keep an eye out for enemy ships. You should be able to stop lone gunmen from picking apart your trade routes, but if a major enemy fleet comes calling, you'll have to respond with your primary attack force.
4.) Use starbases and perimeter defenses to secure the area around your trade routes. Build starbases around the perimeter of your empire and along your trade routes every 10 parasecs or so. Max out their sensor capabilities, add speed modules like Stellar Wake to help your fleets respond faster, and deck out the starbases with trade modules and defenses to eke out the most from your trade routes and keep your starbases safe.